Although that sex change hasn't been really last-minute. It was in the air since the "Open" regulations came out...

The switch from CRT to Open was announced October 2013. January 2014 Ducati was still denying they had any plans to switch the factory team to Open. I realize that as time passed people started suggesting Ducati moving to Open as a desperation move, but early on no one considered it.

Well, actually it was in November 2013 when they announced that Yonny Hernandez would ride with Ducati in 2014 as an Open entry.
Then all the fuss came out only when they decided to enter also the rest of the bikes as Open (and as you wrote it was since January that the word did spread about a possible "switch") but I wonder why nobody complained at the time on Hernandez's bike when technically it was (and is) the same as the Ducatis that now everyone is complaining about...

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My head is my only house unless it rains.D. Van Vliet

... I wonder why nobody complained at the time on Hernandez's bike when technically it was (and is) the same as the Ducatis that now everyone is complaining about...

Cause it was the satellite team. It seems a little different when by Ducati's switch to Open, MotoGP was left in effect with only two factories.

And it would be bad for business if the aliens lost the championship because so much of an advantage was given to the Open class. I hear some talk that Dorna left the door open for Ducati to do what they did in order to speed up the move to control ECUs, but given the unhappiness with 2007's lopsided tire performance, I'm skeptical Dorna would want to go there again for any reason.

The complaints were based on technicalities, and not because there were only two brands competing with Factory rules. Dorna didn't bother. On the contrary they were happy!
And come on, does anyone really thinks that any of the pilots in the Open class have a real shot at winning the championship even with all those advantages?
Take a closer look:
Bikes - they are all running inferior machines (Ducati's TT - older Yammy - Honda slow RCV and old CRT's)
Teams - they are all running with inferior software (it has been said that apart the Ducati team no one knows how to handle the new and improved software)
Riders - they are no "aliens". Put them on the same factory bikes as the really fast guys and they will get beaten by them.
Not a chance.
Truth is Open bikes don't have a chance in winning a single race, let alone the championship. And if it rains or every factory riders is injured they still have Gresini's and LCR's Hondas and Tech3's Yamahas to deal with.
Very hard to get to a podium...

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My head is my only house unless it rains.D. Van Vliet

Yes, in many ways that's more apt. Except that the internet tells me it was the FICM (Fédération Internationale des Clubs Motocyclistes) and the ban predated not only the FIM but the world championship.

And so another alternative is the FIM's pesky and short-sighted restriction of the engine swept volume to 500cc when it set up the world championship for 1949. Which I can guess was aimed at filling the grids, keeping costs down and promoting variety.